2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Softwarechang
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import java.beans.*;
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26 import java.awt.datatransfer.*;
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27 import java.awt.event.*;
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28 import java.awt.print.*;
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29 import javax.swing.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.io.*;
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34 import jalview.jbgui.*;
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35 import jalview.schemes.*;
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36 import jalview.ws.*;
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37 import javax.swing.event.AncestorEvent;
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43 * @version $Revision$
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45 public class AlignFrame
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46 extends GAlignFrame implements ClipboardOwner
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48 /** DOCUMENT ME!! */
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49 public static final int NEW_WINDOW_WIDTH = 700;
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51 /** DOCUMENT ME!! */
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52 public static final int NEW_WINDOW_HEIGHT = 500;
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53 AlignmentPanel alignPanel;
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54 AlignViewport viewport;
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56 Vector viewports = new Vector();
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57 Vector alignPanels = new Vector();
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59 /** DOCUMENT ME!! */
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60 public String currentFileFormat = null;
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61 Stack historyList = new Stack();
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62 Stack redoList = new Stack();
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63 private int treeCount = 0;
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67 * Creates a new AlignFrame object.
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69 * @param al DOCUMENT ME!
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71 public AlignFrame(AlignmentI al)
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73 viewport = new AlignViewport(al);
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74 viewports.add(viewport);
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77 if(viewport.vconsensus==null)
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79 //Out of memory calculating consensus.
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80 BLOSUM62Colour.setEnabled(false);
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81 PIDColour.setEnabled(false);
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82 conservationMenuItem.setEnabled(false);
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83 modifyConservation.setEnabled(false);
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84 abovePIDThreshold.setEnabled(false);
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85 modifyPID.setEnabled(false);
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88 alignPanel = new AlignmentPanel(this, viewport);
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89 alignPanels.add(alignPanel);
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91 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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93 if(sortby.equals("Id"))
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94 sortIDMenuItem_actionPerformed(null);
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95 else if(sortby.equals("Pairwise Identity"))
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96 sortPairwiseMenuItem_actionPerformed(null);
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98 // remove(tabbedPane);
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99 getContentPane().add(alignPanel, BorderLayout.CENTER);
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103 // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
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106 /////////////////////////
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107 if(al.getDataset()==null)
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109 al.setDataset(null);
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111 // AlignViewport ds = new AlignViewport(al.getDataset(), true);
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112 // AlignmentPanel dap = new AlignmentPanel(this, ds);
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113 // tabbedPane.add("Dataset", dap);
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114 // viewports.add(ds);
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115 // alignPanels.add(dap);
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116 /////////////////////////
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119 viewport.addPropertyChangeListener(new PropertyChangeListener()
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121 public void propertyChange(PropertyChangeEvent evt)
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123 if (evt.getPropertyName().equals("alignment"))
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125 alignmentChanged();
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131 if (Desktop.desktop != null)
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133 addServiceListeners();
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134 setGUINucleotide(al.isNucleotide());
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138 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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139 private void addServiceListeners()
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141 final java.beans.PropertyChangeListener thisListener;
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142 // Do this once to get current state
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143 BuildWebServiceMenu();
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144 Desktop.discoverer.addPropertyChangeListener(
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145 thisListener = new java.beans.PropertyChangeListener()
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147 public void propertyChange(PropertyChangeEvent evt)
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149 // System.out.println("Discoverer property change.");
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150 if (evt.getPropertyName().equals("services"))
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152 // System.out.println("Rebuilding web service menu");
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153 BuildWebServiceMenu();
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157 addInternalFrameListener(new javax.swing.event.
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158 InternalFrameAdapter()
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160 public void internalFrameClosed(
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161 javax.swing.event.InternalFrameEvent evt)
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163 // System.out.println("deregistering discoverer listener");
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164 Desktop.discoverer.removePropertyChangeListener(thisListener);
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165 closeMenuItem_actionPerformed(null);
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172 public void setGUINucleotide(boolean nucleotide)
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174 showTranslation.setVisible( nucleotide );
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175 sequenceFeatures.setVisible(!nucleotide );
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176 featureSettings.setVisible( !nucleotide );
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177 conservationMenuItem.setVisible( !nucleotide );
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178 modifyConservation.setVisible( !nucleotide );
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180 //Deal with separators
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181 //Remember AlignFrame always starts as protein
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184 viewMenu.remove(viewMenu.getItemCount()-2);
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188 calculateMenu.remove(calculateMenu.getItemCount()-2);
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194 Added so Castor Mapping file can obtain Jalview Version
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196 public String getVersion()
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198 return jalview.bin.Cache.getProperty("VERSION");
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205 * @param String DOCUMENT ME!
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208 public void parseGroupsFile(String file)
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212 BufferedReader in = new BufferedReader(new FileReader(file));
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213 SequenceI seq = null;
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214 String line, type, desc, token;
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216 int index, start, end;
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217 StringTokenizer st;
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218 SequenceFeature sf;
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219 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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221 while ( (line = in.readLine()) != null)
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224 st = new StringTokenizer(line, "\t");
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225 if (st.countTokens() == 2)
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227 type = st.nextToken();
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228 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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229 fr.setColour(type, ucs.findColour("A"));
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233 while (st.hasMoreElements())
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235 desc = st.nextToken();
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236 token = st.nextToken();
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237 if (!token.equals("ID_NOT_SPECIFIED"))
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239 index = viewport.alignment.findIndex(viewport.alignment.findName(
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245 index = Integer.parseInt(st.nextToken());
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248 start = Integer.parseInt(st.nextToken());
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249 end = Integer.parseInt(st.nextToken());
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251 seq = viewport.alignment.getSequenceAt(index);
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252 start = seq.findIndex(start) - 1;
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253 end = seq.findIndex(end) - 1;
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255 type = st.nextToken();
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257 if (fr.getColour(type) == null)
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259 // Probably the old style groups file
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260 UserColourScheme ucs = new UserColourScheme(type);
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261 fr.setColour(type, ucs.findColour("A"));
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265 sf = new SequenceFeature(type, desc, "", start, end);
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267 seq.addSequenceFeature(sf);
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270 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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271 // sg.addSequence(seq, false);
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273 // viewport.alignment.addGroup(sg);
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278 viewport.showSequenceFeatures = true;
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279 ((Alignment)viewport.alignment).featuresAdded = true;
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281 alignPanel.repaint();
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284 catch (Exception ex)
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286 System.out.println("Error parsing groups file: " + ex);
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290 public void fetchSequence_actionPerformed(ActionEvent e)
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292 new SequenceFetcher(this);
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299 * @param e DOCUMENT ME!
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301 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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303 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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308 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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313 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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314 }, currentFileFormat);
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316 chooser.setAcceptAllFileFilterUsed(false);
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317 chooser.setFileView(new JalviewFileView());
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318 chooser.setDialogTitle("Save Alignment to file");
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319 chooser.setToolTipText("Save");
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321 int value = chooser.showSaveDialog(this);
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323 if (value == JalviewFileChooser.APPROVE_OPTION)
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325 currentFileFormat = chooser.getSelectedFormat();
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327 if (currentFileFormat == null)
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329 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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330 "You must select a file format before saving!",
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331 "File format not specified",
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332 JOptionPane.WARNING_MESSAGE);
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333 value = chooser.showSaveDialog(this);
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337 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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338 currentFileFormat);
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340 String choice = chooser.getSelectedFile().getPath();
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341 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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343 saveAlignment(choice, currentFileFormat);
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347 public boolean saveAlignment(String file, String format)
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349 if (format.equalsIgnoreCase("Jalview"))
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351 String shortName = title;
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353 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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355 shortName = shortName.substring(shortName.lastIndexOf(
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356 java.io.File.separatorChar) + 1);
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359 Jalview2XML.SaveAlignment(this, file, shortName);
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361 // USE Jalview2XML to save this file
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366 String output = new FormatAdapter().formatSequences(format,
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367 viewport.getAlignment().
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369 if (output == null)
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376 java.io.PrintWriter out = new java.io.PrintWriter(
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377 new java.io.FileWriter(file));
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383 catch (Exception ex)
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385 ex.printStackTrace();
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394 * @param e DOCUMENT ME!
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396 protected void outputText_actionPerformed(ActionEvent e)
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398 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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399 Desktop.addInternalFrame(cap,
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400 "Alignment output - " + e.getActionCommand(), 600,
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402 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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403 viewport.getAlignment().
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410 * @param e DOCUMENT ME!
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412 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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414 new HTMLOutput(viewport,
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415 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
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416 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
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419 public void createImageMap(File file, String image)
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421 alignPanel.makePNGImageMap(file, image);
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427 * @param e DOCUMENT ME!
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429 public void createPNG(File f)
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431 alignPanel.makePNG(f);
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437 * @param e DOCUMENT ME!
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439 public void createEPS(File f)
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441 alignPanel.makeEPS(f);
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447 * @param e DOCUMENT ME!
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449 public void printMenuItem_actionPerformed(ActionEvent e)
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451 //Putting in a thread avoids Swing painting problems
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452 PrintThread thread = new PrintThread();
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459 * @param e DOCUMENT ME!
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461 public void closeMenuItem_actionPerformed(ActionEvent e)
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465 PaintRefresher.components.remove(viewport.alignment);
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466 this.setClosed(true);
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468 catch (Exception ex)
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476 void updateEditMenuBar()
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478 if (historyList.size() > 0)
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480 undoMenuItem.setEnabled(true);
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482 HistoryItem hi = (HistoryItem) historyList.peek();
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483 undoMenuItem.setText("Undo " + hi.getDescription());
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487 undoMenuItem.setEnabled(false);
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488 undoMenuItem.setText("Undo");
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491 if (redoList.size() > 0)
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493 redoMenuItem.setEnabled(true);
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495 HistoryItem hi = (HistoryItem) redoList.peek();
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496 redoMenuItem.setText("Redo " + hi.getDescription());
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500 redoMenuItem.setEnabled(false);
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501 redoMenuItem.setText("Redo");
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508 * @param hi DOCUMENT ME!
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510 public void addHistoryItem(HistoryItem hi)
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512 historyList.push(hi);
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513 updateEditMenuBar();
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519 * @param e DOCUMENT ME!
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521 protected void undoMenuItem_actionPerformed(ActionEvent e)
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523 HistoryItem hi = (HistoryItem) historyList.pop();
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524 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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525 HistoryItem.HIDE));
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526 restoreHistoryItem(hi);
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527 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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533 * @param e DOCUMENT ME!
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535 protected void redoMenuItem_actionPerformed(ActionEvent e)
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537 HistoryItem hi = (HistoryItem) redoList.pop();
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538 restoreHistoryItem(hi);
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539 updateEditMenuBar();
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540 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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543 // used by undo and redo
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544 void restoreHistoryItem(HistoryItem hi)
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546 if (hi.getType() == HistoryItem.SORT)
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548 for (int i = 0; i < hi.getSequences().size(); i++)
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550 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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557 for (int i = 0; i < hi.getSequences().size(); i++)
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559 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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561 if (restore.getLength() == 0)
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563 restore.setSequence(hi.getHidden().elementAt(i).toString());
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564 viewport.alignment.getSequences().insertElementAt(restore,
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565 hi.getAlignIndex(i));
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569 restore.setSequence(hi.getHidden().elementAt(i).toString());
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573 if (hi.getType() == HistoryItem.PASTE)
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575 for (int i = viewport.alignment.getHeight() - 1;
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576 i > (hi.getSequences().size() - 1); i--)
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578 viewport.alignment.deleteSequence(i);
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583 updateEditMenuBar();
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585 viewport.firePropertyChange("alignment", null,
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586 viewport.getAlignment().getSequences());
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592 * @param up DOCUMENT ME!
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594 public void moveSelectedSequences(boolean up)
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596 SequenceGroup sg = viewport.getSelectionGroup();
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605 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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607 SequenceI seq = viewport.alignment.getSequenceAt(i);
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609 if (!sg.sequences.contains(seq))
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614 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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616 if (sg.sequences.contains(temp))
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621 viewport.alignment.getSequences().setElementAt(temp, i);
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622 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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627 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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629 SequenceI seq = viewport.alignment.getSequenceAt(i);
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631 if (!sg.sequences.contains(seq))
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636 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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638 if (sg.sequences.contains(temp))
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643 viewport.alignment.getSequences().setElementAt(temp, i);
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644 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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648 alignPanel.repaint();
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651 public void lostOwnership(Clipboard clipboard, Transferable contents)
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653 Desktop.jalviewClipboard = null;
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660 * @param e DOCUMENT ME!
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662 protected void copy_actionPerformed(ActionEvent e)
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664 if (viewport.getSelectionGroup() == null)
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669 SequenceGroup sg = viewport.getSelectionGroup();
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671 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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673 Hashtable orderedSeqs = new Hashtable();
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674 SequenceI[] seqs = new SequenceI[sg.getSize()];
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676 for (int i = 0; i < sg.getSize(); i++)
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678 SequenceI seq = sg.getSequenceAt(i);
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679 int index = viewport.alignment.findIndex(seq);
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680 orderedSeqs.put(index + "", seq);
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683 int index = 0, startRes, endRes;
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686 for (int i = 0; i < sg.getSize(); i++)
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688 SequenceI seq = null;
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690 while (seq == null)
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692 if (orderedSeqs.containsKey(index + ""))
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694 seq = (SequenceI) orderedSeqs.get(index + "");
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706 //Returns residue following index if gap
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707 startRes = seq.findPosition(sg.getStartRes());
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710 //Need to find the residue preceeding index if gap
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713 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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715 ch = seq.getCharAt(j);
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716 if (!jalview.util.Comparison.isGap( (ch)))
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724 endRes += seq.getStart() - 1;
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727 seqs[i] = new Sequence(seq.getName(),
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728 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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731 seqs[i].setDescription(seq.getDescription());
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732 seqs[i].setDBRef(seq.getDBRef());
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733 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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734 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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738 FastaFile ff = new FastaFile();
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739 ff.addDBPrefix( viewport.showDBPrefix );
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740 ff.addJVSuffix( viewport.showJVSuffix );
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741 c.setContents(new StringSelection( ff.print(seqs)), this);
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742 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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748 * @param e DOCUMENT ME!
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750 protected void pasteNew_actionPerformed(ActionEvent e)
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758 * @param e DOCUMENT ME!
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760 protected void pasteThis_actionPerformed(ActionEvent e)
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762 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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763 HistoryItem.PASTE));
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770 * @param newAlignment DOCUMENT ME!
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772 void paste(boolean newAlignment)
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776 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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777 Transferable contents = c.getContents(this);
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779 if (contents == null)
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784 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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788 String format = IdentifyFile.Identify(str, "Paste");
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789 SequenceI[] sequences;
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791 if(Desktop.jalviewClipboard!=null)
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793 // The clipboard was filled from within Jalview, we must use the sequences
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794 // And dataset from the copied alignment
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795 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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799 sequences = new FormatAdapter().readFile(str, "Paste", format);
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805 Alignment alignment = new Alignment(sequences);
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807 if(Desktop.jalviewClipboard!=null)
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808 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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810 alignment.setDataset( null );
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813 AlignFrame af = new AlignFrame(alignment);
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814 String newtitle = new String("Copied sequences");
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816 if (title.startsWith("Copied sequences"))
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822 newtitle = newtitle.concat("- from " + title);
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825 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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826 NEW_WINDOW_HEIGHT);
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831 for (int i = 0; i < sequences.length; i++)
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833 viewport.alignment.addSequence(sequences[i]);
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834 if(sequences[i].getDatasetSequence()==null)
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836 ////////////////////////////
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837 //Datset needs extension;
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838 /////////////////////////////
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839 Sequence ds = new Sequence(sequences[i].getName(),
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840 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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841 sequences[i].getStart(),
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842 sequences[i].getEnd());
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843 sequences[i].setDatasetSequence(ds);
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844 viewport.alignment.getDataset().addSequence(ds);
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850 viewport.setEndSeq(viewport.alignment.getHeight());
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851 viewport.alignment.getWidth();
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852 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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855 catch (Exception ex)
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857 // could be anything being pasted in here
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866 * @param e DOCUMENT ME!
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868 protected void cut_actionPerformed(ActionEvent e)
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870 copy_actionPerformed(null);
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871 delete_actionPerformed(null);
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877 * @param e DOCUMENT ME!
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879 protected void delete_actionPerformed(ActionEvent e)
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882 if (viewport.getSelectionGroup() == null)
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887 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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888 HistoryItem.HIDE));
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890 SequenceGroup sg = viewport.getSelectionGroup();
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891 boolean allSequences = false;
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892 if (sg.sequences.size() == viewport.alignment.getHeight())
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894 allSequences = true;
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897 for (int i = 0; i < sg.sequences.size(); i++)
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899 SequenceI seq = sg.getSequenceAt(i);
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900 int index = viewport.getAlignment().findIndex(seq);
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901 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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903 // If the cut affects all sequences, remove highlighted columns
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906 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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907 sg.getEndRes() + 1);
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910 if (seq.getSequence().length() < 1)
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912 viewport.getAlignment().deleteSequence(seq);
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916 viewport.getAlignment().getSequences().setElementAt(seq, index);
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920 viewport.setSelectionGroup(null);
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921 viewport.alignment.deleteGroup(sg);
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923 viewport.firePropertyChange("alignment", null,
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924 viewport.getAlignment().getSequences());
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928 if (viewport.getAlignment().getHeight() < 1)
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932 this.setClosed(true);
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934 catch (Exception ex)
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943 * @param e DOCUMENT ME!
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945 protected void deleteGroups_actionPerformed(ActionEvent e)
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947 viewport.alignment.deleteAllGroups();
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948 viewport.setSelectionGroup(null);
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949 alignPanel.repaint();
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955 * @param e DOCUMENT ME!
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957 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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959 SequenceGroup sg = new SequenceGroup();
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961 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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964 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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967 sg.setEndRes(viewport.alignment.getWidth() - 1);
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968 viewport.setSelectionGroup(sg);
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969 PaintRefresher.Refresh(null, viewport.alignment);
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975 * @param e DOCUMENT ME!
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977 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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979 viewport.setSelectionGroup(null);
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980 viewport.getColumnSelection().clear();
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981 viewport.setSelectionGroup(null);
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982 alignPanel.annotationPanel.activeRes = null;
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983 PaintRefresher.Refresh(null, viewport.alignment);
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989 * @param e DOCUMENT ME!
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991 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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993 SequenceGroup sg = viewport.getSelectionGroup();
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997 selectAllSequenceMenuItem_actionPerformed(null);
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1002 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1005 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1008 PaintRefresher.Refresh(null, viewport.alignment);
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1014 * @param e DOCUMENT ME!
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1016 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1018 ColumnSelection colSel = viewport.getColumnSelection();
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1020 if (colSel.size() > 0)
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1022 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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1023 HistoryItem.HIDE));
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1025 int min = colSel.getMin();
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1026 viewport.getAlignment().trimLeft(min);
\r
1027 colSel.compensateForEdit(0, min);
\r
1029 if (viewport.getSelectionGroup() != null)
\r
1031 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1034 Vector groups = viewport.alignment.getGroups();
\r
1036 for (int i = 0; i < groups.size(); i++)
\r
1038 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1040 if (!sg.adjustForRemoveLeft(min))
\r
1042 viewport.alignment.deleteGroup(sg);
\r
1046 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1053 * @param e DOCUMENT ME!
\r
1055 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1057 ColumnSelection colSel = viewport.getColumnSelection();
\r
1059 if (colSel.size() > 0)
\r
1061 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1062 HistoryItem.HIDE));
\r
1064 int max = colSel.getMax();
\r
1065 viewport.getAlignment().trimRight(max);
\r
1067 if (viewport.getSelectionGroup() != null)
\r
1069 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1072 Vector groups = viewport.alignment.getGroups();
\r
1074 for (int i = 0; i < groups.size(); i++)
\r
1076 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1078 if (!sg.adjustForRemoveRight(max))
\r
1080 viewport.alignment.deleteGroup(sg);
\r
1084 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1091 * @param e DOCUMENT ME!
\r
1093 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1095 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1096 viewport.alignment, HistoryItem.HIDE));
\r
1098 //This is to maintain viewport position on first residue
\r
1099 //of first sequence
\r
1100 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1101 int startRes = seq.findPosition(viewport.startRes);
\r
1103 viewport.getAlignment().removeGaps();
\r
1105 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1107 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1113 * @param e DOCUMENT ME!
\r
1115 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1117 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1118 HistoryItem.HIDE));
\r
1120 //This is to maintain viewport position on first residue
\r
1121 //of first sequence
\r
1122 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1123 int startRes = seq.findPosition(viewport.startRes);
\r
1126 SequenceI current;
\r
1129 Vector seqs = null;
\r
1132 int end = viewport.alignment.getWidth();
\r
1134 if (viewport.getSelectionGroup() != null
\r
1135 && viewport.getSelectionGroup().sequences != null
\r
1136 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1138 seqs = viewport.getSelectionGroup().sequences;
\r
1139 start = viewport.getSelectionGroup().getStartRes();
\r
1140 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1144 seqs = viewport.alignment.getSequences();
\r
1147 for (int i = 0; i < seqs.size(); i++)
\r
1149 current = (SequenceI) seqs.elementAt(i);
\r
1150 jSize = current.getLength();
\r
1152 // Removing a range is much quicker than removing gaps
\r
1153 // one by one for long sequences
\r
1155 int rangeStart=-1, rangeEnd=-1;
\r
1159 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1161 if(rangeStart==-1)
\r
1176 current.deleteChars(rangeStart, rangeEnd);
\r
1177 j-=rangeEnd-rangeStart;
\r
1178 jSize-=rangeEnd-rangeStart;
\r
1186 while (j < end && j < jSize);
\r
1189 current.deleteChars(rangeStart, rangeEnd);
\r
1193 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1195 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1198 public void alignmentChanged()
\r
1200 if(viewport.vconsensus!=null)
\r
1202 viewport.updateConsensus();
\r
1203 viewport.updateConservation();
\r
1205 resetAllColourSchemes();
\r
1206 if(alignPanel.overviewPanel!=null)
\r
1207 alignPanel.overviewPanel.updateOverviewImage();
\r
1209 Provenance prov = viewport.alignment.getProvenance();
\r
1212 prov = new Provenance();
\r
1213 viewport.alignment.setProvenance(prov);
\r
1216 prov.addEntry("Me",
\r
1217 "Edited in Jalview", new java.util.Date(), "myID");
\r
1219 alignPanel.repaint();
\r
1222 void resetAllColourSchemes()
\r
1224 ColourSchemeI cs = viewport.globalColourScheme;
\r
1227 if (cs instanceof ClustalxColourScheme)
\r
1229 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1230 resetClustalX(viewport.alignment.getSequences(),
\r
1231 viewport.alignment.getWidth());
\r
1234 cs.setConsensus(viewport.vconsensus);
\r
1235 if (cs.conservationApplied())
\r
1237 Alignment al = (Alignment) viewport.alignment;
\r
1238 Conservation c = new Conservation("All",
\r
1239 ResidueProperties.propHash, 3,
\r
1240 al.getSequences(), 0,
\r
1241 al.getWidth() - 1);
\r
1243 c.verdict(false, viewport.ConsPercGaps);
\r
1245 cs.setConservation(c);
\r
1249 int s, sSize = viewport.alignment.getGroups().size();
\r
1250 for(s=0; s<sSize; s++)
\r
1252 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1253 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1255 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1257 sg.recalcConservation();
\r
1264 * @param e DOCUMENT ME!
\r
1266 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1268 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1269 HistoryItem.HIDE));
\r
1271 SequenceI current;
\r
1272 int Width = viewport.getAlignment().getWidth();
\r
1274 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1277 current = viewport.getAlignment().getSequenceAt(i);
\r
1279 if (current.getLength() < Width)
\r
1281 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1285 alignmentChanged();
\r
1291 * @param e DOCUMENT ME!
\r
1293 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1295 JInternalFrame frame = new JInternalFrame();
\r
1296 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1297 frame.setContentPane(finder);
\r
1298 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1299 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1305 * @param e DOCUMENT ME!
\r
1307 public void font_actionPerformed(ActionEvent e)
\r
1309 new FontChooser(alignPanel);
\r
1315 * @param e DOCUMENT ME!
\r
1317 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1319 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1321 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1322 alignPanel.repaint();
\r
1325 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1327 viewport.setShowDBPrefix(seqDBRef.isSelected());
\r
1329 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1330 alignPanel.repaint();
\r
1337 * @param e DOCUMENT ME!
\r
1339 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1341 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1342 alignPanel.repaint();
\r
1348 * @param e DOCUMENT ME!
\r
1350 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1352 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1353 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1354 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1355 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1356 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1357 alignPanel.repaint();
\r
1363 * @param e DOCUMENT ME!
\r
1365 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1367 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1368 alignPanel.repaint();
\r
1374 * @param e DOCUMENT ME!
\r
1376 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1378 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1379 alignPanel.repaint();
\r
1385 * @param e DOCUMENT ME!
\r
1387 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1389 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1390 alignPanel.repaint();
\r
1396 * @param e DOCUMENT ME!
\r
1398 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1400 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1401 alignPanel.repaint();
\r
1407 * @param e DOCUMENT ME!
\r
1409 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1411 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1412 alignPanel.repaint();
\r
1418 * @param e DOCUMENT ME!
\r
1420 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1422 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1423 alignPanel.repaint();
\r
1429 * @param evt DOCUMENT ME!
\r
1431 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1433 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1435 if (viewport.showSequenceFeatures &&
\r
1436 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1438 System.out.println("new fetcher");
\r
1439 new SequenceFeatureFetcher(viewport.
\r
1444 featureSettings.setEnabled(true);
\r
1446 alignPanel.repaint();
\r
1452 * @param e DOCUMENT ME!
\r
1454 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1456 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1457 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1463 * @param e DOCUMENT ME!
\r
1465 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1467 if (alignPanel.overviewPanel != null)
\r
1472 JInternalFrame frame = new JInternalFrame();
\r
1473 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1474 frame.setContentPane(overview);
\r
1475 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1476 frame.getWidth(), frame.getHeight());
\r
1478 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1479 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1481 public void internalFrameClosed(
\r
1482 javax.swing.event.InternalFrameEvent evt)
\r
1484 alignPanel.setOverviewPanel(null);
\r
1489 alignPanel.setOverviewPanel(overview);
\r
1495 * @param e DOCUMENT ME!
\r
1497 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1499 changeColour(null);
\r
1505 * @param e DOCUMENT ME!
\r
1507 public void clustalColour_actionPerformed(ActionEvent e)
\r
1509 changeColour(new ClustalxColourScheme(
\r
1510 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1516 * @param e DOCUMENT ME!
\r
1518 public void zappoColour_actionPerformed(ActionEvent e)
\r
1520 changeColour(new ZappoColourScheme());
\r
1526 * @param e DOCUMENT ME!
\r
1528 public void taylorColour_actionPerformed(ActionEvent e)
\r
1530 changeColour(new TaylorColourScheme());
\r
1536 * @param e DOCUMENT ME!
\r
1538 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1540 changeColour(new HydrophobicColourScheme());
\r
1546 * @param e DOCUMENT ME!
\r
1548 public void helixColour_actionPerformed(ActionEvent e)
\r
1550 changeColour(new HelixColourScheme());
\r
1556 * @param e DOCUMENT ME!
\r
1558 public void strandColour_actionPerformed(ActionEvent e)
\r
1560 changeColour(new StrandColourScheme());
\r
1566 * @param e DOCUMENT ME!
\r
1568 public void turnColour_actionPerformed(ActionEvent e)
\r
1570 changeColour(new TurnColourScheme());
\r
1576 * @param e DOCUMENT ME!
\r
1578 public void buriedColour_actionPerformed(ActionEvent e)
\r
1580 changeColour(new BuriedColourScheme());
\r
1586 * @param e DOCUMENT ME!
\r
1588 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1590 changeColour(new NucleotideColourScheme());
\r
1596 * @param e DOCUMENT ME!
\r
1598 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1600 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1606 * @param cs DOCUMENT ME!
\r
1608 void changeColour(ColourSchemeI cs)
\r
1610 int threshold = 0;
\r
1614 if (viewport.getAbovePIDThreshold())
\r
1616 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1619 cs.setThreshold(threshold,
\r
1620 viewport.getIgnoreGapsConsensus());
\r
1622 viewport.setGlobalColourScheme(cs);
\r
1626 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1629 if (viewport.getConservationSelected())
\r
1632 Alignment al = (Alignment) viewport.alignment;
\r
1633 Conservation c = new Conservation("All",
\r
1634 ResidueProperties.propHash, 3,
\r
1635 al.getSequences(), 0,
\r
1636 al.getWidth() - 1);
\r
1639 c.verdict(false, viewport.ConsPercGaps);
\r
1641 cs.setConservation(c);
\r
1643 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1648 cs.setConservation(null);
\r
1651 cs.setConsensus(viewport.vconsensus);
\r
1654 viewport.setGlobalColourScheme(cs);
\r
1656 if (viewport.getColourAppliesToAllGroups())
\r
1658 Vector groups = viewport.alignment.getGroups();
\r
1660 for (int i = 0; i < groups.size(); i++)
\r
1662 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1670 if (cs instanceof ClustalxColourScheme)
\r
1672 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1674 else if (cs instanceof UserColourScheme)
\r
1676 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1682 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1684 catch (Exception ex)
\r
1689 if (viewport.getAbovePIDThreshold()
\r
1690 || cs instanceof PIDColourScheme
\r
1691 || cs instanceof Blosum62ColourScheme)
\r
1693 sg.cs.setThreshold(threshold,
\r
1694 viewport.getIgnoreGapsConsensus());
\r
1696 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1700 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1703 if (viewport.getConservationSelected())
\r
1705 Conservation c = new Conservation("Group",
\r
1706 ResidueProperties.propHash, 3,
\r
1708 viewport.alignment.getWidth() - 1);
\r
1710 c.verdict(false, viewport.ConsPercGaps);
\r
1711 sg.cs.setConservation(c);
\r
1714 sg.cs.setConservation(null);
\r
1718 if (alignPanel.getOverviewPanel() != null)
\r
1720 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1723 alignPanel.repaint();
\r
1729 * @param e DOCUMENT ME!
\r
1731 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1733 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1735 SliderPanel.setPIDSliderSource(alignPanel,
\r
1736 viewport.getGlobalColourScheme(),
\r
1738 SliderPanel.showPIDSlider();
\r
1745 * @param e DOCUMENT ME!
\r
1747 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1749 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1751 SliderPanel.setConservationSlider(alignPanel,
\r
1752 viewport.globalColourScheme,
\r
1754 SliderPanel.showConservationSlider();
\r
1761 * @param e DOCUMENT ME!
\r
1763 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1765 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1767 viewport.setAbovePIDThreshold(false);
\r
1768 abovePIDThreshold.setSelected(false);
\r
1770 changeColour(viewport.getGlobalColourScheme());
\r
1772 modifyConservation_actionPerformed(null);
\r
1778 * @param e DOCUMENT ME!
\r
1780 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1782 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1784 conservationMenuItem.setSelected(false);
\r
1785 viewport.setConservationSelected(false);
\r
1787 changeColour(viewport.getGlobalColourScheme());
\r
1789 modifyPID_actionPerformed(null);
\r
1795 * @param e DOCUMENT ME!
\r
1797 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1799 if (e.getActionCommand().equals("User Defined..."))
\r
1801 new UserDefinedColours(alignPanel, null);
\r
1805 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1806 getUserColourSchemes().get(e.getActionCommand());
\r
1808 changeColour(udc);
\r
1812 public void updateUserColourMenu()
\r
1815 Component[] menuItems = colourMenu.getMenuComponents();
\r
1816 int i, iSize = menuItems.length;
\r
1817 for (i = 0; i < iSize; i++)
\r
1819 if (menuItems[i].getName() != null &&
\r
1820 menuItems[i].getName().equals("USER_DEFINED"))
\r
1822 colourMenu.remove(menuItems[i]);
\r
1826 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1828 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1829 getUserColourSchemes().keys();
\r
1831 while (userColours.hasMoreElements())
\r
1833 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1834 nextElement().toString());
\r
1835 radioItem.setName("USER_DEFINED");
\r
1836 radioItem.addMouseListener(new MouseAdapter()
\r
1838 public void mousePressed(MouseEvent evt)
\r
1840 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1842 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1844 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1845 "Remove from default list?",
\r
1846 "Remove user defined colour",
\r
1847 JOptionPane.YES_NO_OPTION);
\r
1848 if(option == JOptionPane.YES_OPTION)
\r
1850 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1851 colourMenu.remove(radioItem);
\r
1854 radioItem.addActionListener(new ActionListener()
\r
1856 public void actionPerformed(ActionEvent evt)
\r
1858 userDefinedColour_actionPerformed(evt);
\r
1864 radioItem.addActionListener(new ActionListener()
\r
1866 public void actionPerformed(ActionEvent evt)
\r
1868 userDefinedColour_actionPerformed(evt);
\r
1872 colourMenu.insert(radioItem, 15);
\r
1873 colours.add(radioItem);
\r
1881 * @param e DOCUMENT ME!
\r
1883 public void PIDColour_actionPerformed(ActionEvent e)
\r
1885 changeColour(new PIDColourScheme());
\r
1891 * @param e DOCUMENT ME!
\r
1893 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1895 changeColour(new Blosum62ColourScheme());
\r
1901 * @param e DOCUMENT ME!
\r
1903 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1905 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1906 HistoryItem.SORT));
\r
1907 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1908 viewport.getAlignment().getSequenceAt(0));
\r
1909 alignPanel.repaint();
\r
1915 * @param e DOCUMENT ME!
\r
1917 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1919 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1920 HistoryItem.SORT));
\r
1921 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1922 alignPanel.repaint();
\r
1928 * @param e DOCUMENT ME!
\r
1930 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1932 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1933 HistoryItem.SORT));
\r
1935 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1936 alignPanel.repaint();
\r
1942 * @param e DOCUMENT ME!
\r
1944 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1946 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1947 JInternalFrame frame = new JInternalFrame();
\r
1948 frame.setContentPane(sp);
\r
1949 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1956 * @param e DOCUMENT ME!
\r
1958 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1960 if ( (viewport.getSelectionGroup() == null) ||
\r
1961 (viewport.getSelectionGroup().getSize() < 2))
\r
1963 JOptionPane.showInternalMessageDialog(this,
\r
1964 "You must select at least 2 sequences.",
\r
1965 "Invalid Selection",
\r
1966 JOptionPane.WARNING_MESSAGE);
\r
1970 JInternalFrame frame = new JInternalFrame();
\r
1971 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1972 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1979 * @param e DOCUMENT ME!
\r
1981 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1983 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1984 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1985 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1986 (viewport.getAlignment().getHeight() < 4))
\r
1988 JOptionPane.showInternalMessageDialog(this,
\r
1989 "Principal component analysis must take\n" +
\r
1990 "at least 4 input sequences.",
\r
1991 "Sequence selection insufficient",
\r
1992 JOptionPane.WARNING_MESSAGE);
\r
1997 new PCAPanel(viewport);
\r
2003 * @param e DOCUMENT ME!
\r
2005 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
2007 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2013 * @param e DOCUMENT ME!
\r
2015 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
2017 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2023 * @param e DOCUMENT ME!
\r
2025 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2027 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2033 * @param e DOCUMENT ME!
\r
2035 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2037 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2043 * @param type DOCUMENT ME!
\r
2044 * @param pwType DOCUMENT ME!
\r
2045 * @param title DOCUMENT ME!
\r
2047 void NewTreePanel(String type, String pwType, String title)
\r
2049 final TreePanel tp;
\r
2051 if ( (viewport.getSelectionGroup() != null) &&
\r
2052 (viewport.getSelectionGroup().getSize() > 3))
\r
2055 SequenceGroup sg = viewport.getSelectionGroup();
\r
2057 /* Decide if the selection is a column region */
\r
2058 while (s < sg.sequences.size())
\r
2060 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2063 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2064 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2065 "Try using the Pad function in the edit menu,\n" +
\r
2066 "or one of the multiple sequence alignment web services.",
\r
2067 "Sequences in selection are not aligned",
\r
2068 JOptionPane.WARNING_MESSAGE);
\r
2074 title = title + " on region";
\r
2075 tp = new TreePanel(viewport,
\r
2076 viewport.getSelectionGroup().sequences, type, pwType,
\r
2077 sg.getStartRes(), sg.getEndRes());
\r
2081 //are the sequences aligned?
\r
2082 if (!viewport.alignment.isAligned())
\r
2084 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2085 "The sequences must be aligned before creating a tree.\n" +
\r
2086 "Try using the Pad function in the edit menu,\n" +
\r
2087 "or one of the multiple sequence alignment web services.",
\r
2088 "Sequences not aligned",
\r
2089 JOptionPane.WARNING_MESSAGE);
\r
2094 tp = new TreePanel(viewport,
\r
2095 viewport.getAlignment().getSequences(), type, pwType,
\r
2097 viewport.alignment.getWidth());
\r
2100 addTreeMenuItem(tp, title);
\r
2101 viewport.setCurrentTree(tp.getTree());
\r
2103 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2109 * @param title DOCUMENT ME!
\r
2110 * @param order DOCUMENT ME!
\r
2112 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2114 final JMenuItem item = new JMenuItem("by " + title);
\r
2116 item.addActionListener(new java.awt.event.ActionListener()
\r
2118 public void actionPerformed(ActionEvent e)
\r
2120 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2121 HistoryItem.SORT));
\r
2123 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2124 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2125 alignPanel.repaint();
\r
2131 * Maintain the Order by->Displayed Tree menu.
\r
2132 * Creates a new menu item for a TreePanel with an appropriate
\r
2133 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2134 * to remove the menu item when the treePanel is closed, and adjust
\r
2135 * the tree leaf to sequence mapping when the alignment is modified.
\r
2136 * @param treePanel Displayed tree window.
\r
2137 * @param title SortBy menu item title.
\r
2139 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2141 final JMenuItem item = new JMenuItem(title);
\r
2145 if (treeCount == 1)
\r
2147 sort.add(sortByTreeMenu);
\r
2150 sortByTreeMenu.add(item);
\r
2151 item.addActionListener(new java.awt.event.ActionListener()
\r
2153 public void actionPerformed(ActionEvent e)
\r
2155 addHistoryItem(new HistoryItem("Tree Sort",
\r
2156 viewport.alignment, HistoryItem.SORT));
\r
2157 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2158 treePanel.getTree());
\r
2159 alignPanel.repaint();
\r
2163 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2164 InternalFrameAdapter()
\r
2166 public void internalFrameClosed(
\r
2167 javax.swing.event.InternalFrameEvent evt)
\r
2170 sortByTreeMenu.remove(item);
\r
2172 if (treeCount == 0)
\r
2174 sort.remove(sortByTreeMenu);
\r
2182 * Work out whether the whole set of sequences
\r
2183 * or just the selected set will be submitted for multiple alignment.
\r
2186 private SequenceI[] gatherSequencesForAlignment()
\r
2188 // Now, check we have enough sequences
\r
2189 SequenceI[] msa = null;
\r
2191 if ( (viewport.getSelectionGroup() != null) &&
\r
2192 (viewport.getSelectionGroup().getSize() > 1))
\r
2194 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2195 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2197 msa = new SequenceI[sz = seqs.getSize()];
\r
2199 for (int i = 0; i < sz; i++)
\r
2201 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2206 Vector seqs = viewport.getAlignment().getSequences();
\r
2208 if (seqs.size() > 1)
\r
2210 msa = new SequenceI[seqs.size()];
\r
2212 for (int i = 0; i < seqs.size(); i++)
\r
2214 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2222 * Decides what is submitted to a secondary structure prediction service,
\r
2223 * the currently selected sequence, or the currently selected alignment
\r
2224 * (where the first sequence in the set is the one that the prediction
\r
2227 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2229 SequenceI seq = null;
\r
2230 SequenceI[] msa = null;
\r
2232 if ( (viewport.getSelectionGroup() != null) &&
\r
2233 (viewport.getSelectionGroup().getSize() > 0))
\r
2235 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2236 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2238 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2240 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2245 msa = new SequenceI[sz = seqs.getSize()];
\r
2247 for (int i = 0; i < sz; i++)
\r
2249 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2255 Vector seqs = viewport.getAlignment().getSequences();
\r
2257 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2259 seq = (SequenceI) seqs.elementAt(0);
\r
2263 msa = new SequenceI[seqs.size()];
\r
2265 for (int i = 0; i < seqs.size(); i++)
\r
2267 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2279 return new SequenceI[]
\r
2289 * @param e DOCUMENT ME!
\r
2291 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2293 // Pick the tree file
\r
2294 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2296 "LAST_DIRECTORY"));
\r
2297 chooser.setFileView(new JalviewFileView());
\r
2298 chooser.setDialogTitle("Select a newick-like tree file");
\r
2299 chooser.setToolTipText("Load a tree file");
\r
2301 int value = chooser.showOpenDialog(null);
\r
2303 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2305 String choice = chooser.getSelectedFile().getPath();
\r
2306 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2310 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2312 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2314 catch (Exception ex)
\r
2316 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2317 "Problem reading tree file",
\r
2319 JOptionPane.WARNING_MESSAGE);
\r
2320 ex.printStackTrace();
\r
2326 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2328 return ShowNewickTree(nf,title,600,500,4,5);
\r
2333 * @param nf DOCUMENT ME!
\r
2334 * @param title DOCUMENT ME!
\r
2336 * @return DOCUMENT ME!
\r
2338 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2340 TreePanel tp = null;
\r
2346 if (nf.getTree() != null)
\r
2348 tp = new TreePanel(viewport,
\r
2349 viewport.getAlignment().getSequences(), nf,
\r
2356 tp.setLocation(x,y);
\r
2359 Desktop.addInternalFrame(tp, title, w, h);
\r
2360 addTreeMenuItem(tp, title);
\r
2363 catch (Exception ex)
\r
2365 ex.printStackTrace();
\r
2376 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2377 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2378 printJob.setPrintable(alignPanel, pf);
\r
2380 if (printJob.printDialog())
\r
2386 catch (Exception PrintException)
\r
2388 PrintException.printStackTrace();
\r
2395 * Generates menu items and listener event actions for web service clients
\r
2398 public void BuildWebServiceMenu()
\r
2400 if ( (Discoverer.services != null)
\r
2401 && (Discoverer.services.size() > 0))
\r
2403 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2404 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2405 Vector wsmenu = new Vector();
\r
2406 if (msaws != null)
\r
2408 // Add any Multiple Sequence Alignment Services
\r
2409 final JMenu msawsmenu = new JMenu("Alignment");
\r
2410 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2412 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2414 final JMenuItem method = new JMenuItem(sh.getName());
\r
2415 method.addActionListener(new ActionListener()
\r
2417 public void actionPerformed(ActionEvent e)
\r
2419 SequenceI[] msa = gatherSequencesForAlignment();
\r
2420 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2421 false, true, viewport.getAlignment().getDataset());
\r
2426 msawsmenu.add(method);
\r
2427 // Deal with services that we know accept partial alignments.
\r
2428 if (sh.getName().indexOf("lustal") > -1)
\r
2430 // We know that ClustalWS can accept partial alignments for refinement.
\r
2431 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2432 methodR.addActionListener(new ActionListener()
\r
2434 public void actionPerformed(ActionEvent e)
\r
2436 SequenceI[] msa = gatherSequencesForAlignment();
\r
2437 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2438 true, true, viewport.getAlignment().getDataset());
\r
2443 msawsmenu.add(methodR);
\r
2447 wsmenu.add(msawsmenu);
\r
2449 if (secstrpr != null)
\r
2451 // Add any secondary structure prediction services
\r
2452 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2453 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2455 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2457 final JMenuItem method = new JMenuItem(sh.getName());
\r
2458 method.addActionListener(new ActionListener()
\r
2460 public void actionPerformed(ActionEvent e)
\r
2462 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2463 if (msa.length == 1)
\r
2465 // Single Sequence prediction
\r
2466 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2470 if (msa.length > 1)
\r
2472 // Single Sequence prediction
\r
2473 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2479 secstrmenu.add(method);
\r
2481 wsmenu.add(secstrmenu);
\r
2483 this.webService.removeAll();
\r
2484 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2486 webService.add( (JMenu) wsmenu.get(i));
\r
2491 this.webService.removeAll();
\r
2492 this.webService.add(this.webServiceNoServices);
\r
2494 // TODO: add in rediscovery function
\r
2495 // TODO: reduce code redundancy.
\r
2496 // TODO: group services by location as well as function.
\r
2499 /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
2501 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2502 getProperty("LAST_DIRECTORY"));
\r
2504 chooser.setFileView(new JalviewFileView());
\r
2505 chooser.setDialogTitle("Export to Vamsas file");
\r
2506 chooser.setToolTipText("Export");
\r
2508 int value = chooser.showSaveDialog(this);
\r
2510 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2512 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2513 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2514 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2518 public void featureSettings_actionPerformed(ActionEvent e)
\r
2520 new FeatureSettings(viewport, alignPanel);
\r
2525 public void showTranslation_actionPerformed(ActionEvent e)
\r
2527 int s, sSize = viewport.alignment.getHeight();
\r
2528 SequenceI [] newSeq = new SequenceI[sSize];
\r
2531 StringBuffer protein;
\r
2533 for(s=0; s<sSize; s++)
\r
2535 protein = new StringBuffer();
\r
2536 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2537 resSize = seq.length();
\r
2538 for(res = 0; res < resSize; res+=3)
\r
2540 String codon = seq.substring(res, res+3);
\r
2541 codon = codon.replace('U', 'T');
\r
2542 String aa = ResidueProperties.codonTranslate(codon);
\r
2544 protein.append(viewport.getGapCharacter());
\r
2545 else if(aa.equals("STOP"))
\r
2546 protein.append("X");
\r
2548 protein.append( aa );
\r
2550 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2554 AlignmentI al = new Alignment(newSeq);
\r
2555 al.setDataset(null);
\r
2558 ////////////////////////////////
\r
2559 // Copy annotations across
\r
2560 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2561 = viewport.alignment.getAlignmentAnnotation();
\r
2563 for (int i = 0; i < annotations.length; i++)
\r
2566 if (annotations[i].label.equals("Quality") ||
\r
2567 annotations[i].label.equals("Conservation") ||
\r
2568 annotations[i].label.equals("Consensus"))
\r
2574 aSize = viewport.alignment.getWidth()/3;
\r
2575 jalview.datamodel.Annotation [] anots =
\r
2576 new jalview.datamodel.Annotation[aSize];
\r
2578 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2580 if( annotations[i].annotations[a]==null
\r
2581 || annotations[i].annotations[a]==null)
\r
2584 anots[a/3] = new Annotation(
\r
2585 annotations[i].annotations[a].displayCharacter,
\r
2586 annotations[i].annotations[a].description,
\r
2587 annotations[i].annotations[a].secondaryStructure,
\r
2588 annotations[i].annotations[a].value,
\r
2589 annotations[i].annotations[a].colour);
\r
2592 jalview.datamodel.AlignmentAnnotation aa
\r
2593 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2594 annotations[i].description, anots );
\r
2595 al.addAnnotation(aa);
\r
2599 AlignFrame af = new AlignFrame(al);
\r
2600 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2602 NEW_WINDOW_HEIGHT);
\r
2605 // AlignViewport newViewport = new AlignViewport(al);
\r
2606 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2607 // tabbedPane.add("Protein", ap);
\r
2608 // viewports.add(newViewport);
\r
2609 // alignPanels.add(ap);
\r
2612 /////////////////////////
\r
2614 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2615 // ds.setDataset(true);
\r
2616 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2617 // tabbedPane.add("Dataset", dap);
\r
2618 // viewports.add(ds);
\r
2619 // alignPanels.add(dap);
\r
2620 /////////////////////////
\r
2625 /*public void tabSelected()
\r
2627 int index = tabbedPane.getSelectedIndex();
\r
2628 viewport = (AlignViewport)viewports.elementAt(index);
\r
2629 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r